Mercurial > repos > iuc > package_tabix_0_2_6
comparison tool_dependencies.xml @ 0:c1743e071a28 draft
Imported from capsule None
| author | iuc |
|---|---|
| date | Wed, 06 Aug 2014 17:19:24 -0400 |
| parents | |
| children | 54f8b9bf9b6c |
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| -1:000000000000 | 0:c1743e071a28 |
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| 1 <?xml version="1.0"?> | |
| 2 <tool_dependency> | |
| 3 <package name="tabix" version="0.2.6"> | |
| 4 <install version="1.0"> | |
| 5 <actions> | |
| 6 <action type="download_by_url">http://sourceforge.net/projects/samtools/files/tabix/tabix-0.2.6.tar.bz2</action> | |
| 7 <action type="shell_command">make</action> | |
| 8 <action type="move_file"> | |
| 9 <source>tabix</source> | |
| 10 <destination>$INSTALL_DIR/bin</destination> | |
| 11 </action> | |
| 12 <action type="move_file"> | |
| 13 <source>bgzip</source> | |
| 14 <destination>$INSTALL_DIR/bin</destination> | |
| 15 </action> | |
| 16 <action type="set_environment"> | |
| 17 <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR/bin</environment_variable> | |
| 18 <environment_variable name="TABIX_BIN_PATH" action="set_to">$INSTALL_DIR/bin</environment_variable> | |
| 19 </action> | |
| 20 </actions> | |
| 21 </install> | |
| 22 <readme> | |
| 23 Installs tabix version 0.2.6. Available binaries: tabix, bgzip | |
| 24 http://samtools.sourceforge.net/tabix.shtml | |
| 25 | |
| 26 Tabix indexes a TAB-delimited genome position file in.tab.bgz and creates an index file in.tab.bgz.tbi when region is absent from the command-line. | |
| 27 The input data file must be position sorted and compressed by bgzip which has a gzip(1) like interface. After indexing, | |
| 28 tabix is able to quickly retrieve data lines overlapping regions specified in the format "chr:beginPos-endPos". | |
| 29 Fast data retrieval also works over network if URI is given as a file name and in this case the index file will be downloaded if it is not present locally. | |
| 30 </readme> | |
| 31 </package> | |
| 32 </tool_dependency> |